GATK

两个工具：UnifiedGenotyper
Can’t get calls for multiple records at same position in the alleles input file; UnifiedGenotyper
One way is to separate out the SNPs and indels then re-merge them.
这是UG的硬伤呀，如果生成vcf中有两个点位置一样，则只能call其中一个，插入或删除突变的位置跟点突变的位置一样，则只能call 点突变，所以他们才建议插入删除突变单独跑
http://gatkforums.broadinstitute.org/gatk/discussion/2305/cant-get-calls-for-multiple-records-at-same-position-in-the-alleles-input-file-unifiedgenotyper